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| Code Block |
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| language | bash |
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| title | my_job.pbs |
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#!/bin/bash
#PBS -<parametar1> <value>
#PBS -<parametar2> <value>
<command> |
Basic PBS parameters
| Option | Argument | Meaning |
-N | name | Naming the job |
-q | destination | Specifying job queue or node |
-l | list_of_resources | Amount of resources required for the job |
-M | list_of_users | List of users to receive e-mail |
-m | email_options | Types of mail notifications |
-o | path/to/directory | Path to directory for output file |
-e | path/to/directory | Path to directory for error file |
-j
| oe | Combining output and error file |
| -Wgroup_list | project_code | Project code for job |
Options for sending notifications by mail with the -m option:
| a | Mail is sent when the batch system terminates the job |
| b | Mail is sent when the job starts executing |
| e | Mail is sent when the job is done |
| j | Mail is sent for sub jobs. Must be combined with one or more sub-options a, b or e |
| Code Block |
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| language | bash |
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| title | Example mail |
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#!/bin/bash
#PBS -q cpu
#PBS -l select=1:ncpus=2
#PBS -M <name>@srce.hr,<name2>@srce.hr
#PBS -m be
echo $PBS_JOBNAME > out
echo $PBS_O_HOST |
Two emails were received:
| Code Block |
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PBS Job Id: 2686.x3000c0s25b0n0.hsn.hpc.srce.hr
Job Name: pbs.pbs
Begun execution |
| Code Block |
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PBS Job Id: 2686.x3000c0s25b0n0.hsn.hpc.srce.hr
Job Name: pbs.pbs
Execution terminated
Exit_status=0
resources_used.cpupercent=0
resources_used.cput=00:00:00
resources_used.mem=0kb
resources_used.ncpus=2
resources_used.vmem=0kb
resources_used.walltime=00:00:01 |
Options for resources with the -l option:
| -l select=3:ncpus=2 | Option for 3 chunks of a node with 2 cores (6 cores in total) |
| -l select=1:ncpus=10:mem=20GB | Option for 1 chunka of a node with 10 cores i 20GB RAM |
| -l ngpus=2 | Option for 2 GPU-s |
PBS environmental variables
| NCPUS | Number of cores requested. Matches the value from the ncpus option from the PBS script header. |
| OMP_NUM_THREADS | An OpenMP variable exported by PBS to the environment that is equal to the value of the ncpus option from the PBS script header |
| PBS_JOBID | Identifikator posla koji daje PBS kada se posao preda. Stvoreno nakon izvršenja naredbe qsub.
|
| PBS_JOBNAME | Job identifier provided by PBS when a job is submitted. Created after executing the qsub command. |
| PBS_NODEFILE | List of work nodes, or processor cores on which the job is executed |
| PBS_O_WORKDIR | The working directory in which the job was submitted, or in which the qsub command was invoked. |
| TMPDIR | The path to the scratch directory. |
| Tip |
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| title | Setting up working directory |
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While in PBS pro the path for output and error files is specified in the directory where they are executed, the input and output files of the program itself are by default loaded/saved in the $HOME directory. PBS Pro does not have the option of specifying the job to run in the current directory we are in, so it is necessary to manually change the directory. After the header it is necessary to write: cd $PBS_O_WORKDIR It will redirect the job execution to the directory where the script was run. |
